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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 35175

FusionGeneSummary for SNRNP40_PEF1

check button Fusion gene summary
Fusion gene informationFusion gene name: SNRNP40_PEF1
Fusion gene ID: 35175
HgeneTgene
Gene symbol

SNRNP40

PEF1

Gene ID

9410

553115

Gene namesmall nuclear ribonucleoprotein U5 subunit 40penta-EF-hand domain containing 1
Synonyms40K|HPRP8BP|PRP8BP|PRPF8BP|SPF38|WDR57ABP32|PEF1A
Cytomap

1p35.2

1p35.2

Type of geneprotein-codingprotein-coding
DescriptionU5 small nuclear ribonucleoprotein 40 kDa protein38 kDa-splicing factorPrp8-binding proteinU5 snRNP 40 kDa proteinU5 snRNP-specific 40 kDa protein (hPrp8-binding)U5-40KU5-40kD proteinWD repeat domain 57 (U5 snRNP specific)WD repeat-containing protpeflinPEF protein with a long N-terminal hydrophobic domain
Modification date2018052320180522
UniProtAcc

Q96DI7

Q9UBV8

Ensembl transtripts involved in fusion geneENST00000263694, ENST00000489853, 
ENST00000373720, ENST00000446633, 
ENST00000373703, ENST00000492061, 
ENST00000440872, 
Fusion gene scores* DoF score6 X 3 X 5=901 X 1 X 1=1
# samples 51
** MAII scorelog2(5/90*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: SNRNP40 [Title/Abstract] AND PEF1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID

check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVUCECTCGA-H5-A2HR-01ASNRNP40chr1

31762101

-PEF1chr1

32101123

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000263694ENST00000373703SNRNP40chr1

31762101

-PEF1chr1

32101123

-
5CDS-5UTRENST00000263694ENST00000492061SNRNP40chr1

31762101

-PEF1chr1

32101123

-
5CDS-5UTRENST00000263694ENST00000440872SNRNP40chr1

31762101

-PEF1chr1

32101123

-
intron-3CDSENST00000489853ENST00000373703SNRNP40chr1

31762101

-PEF1chr1

32101123

-
intron-5UTRENST00000489853ENST00000492061SNRNP40chr1

31762101

-PEF1chr1

32101123

-
intron-5UTRENST00000489853ENST00000440872SNRNP40chr1

31762101

-PEF1chr1

32101123

-
intron-3CDSENST00000373720ENST00000373703SNRNP40chr1

31762101

-PEF1chr1

32101123

-
intron-5UTRENST00000373720ENST00000492061SNRNP40chr1

31762101

-PEF1chr1

32101123

-
intron-5UTRENST00000373720ENST00000440872SNRNP40chr1

31762101

-PEF1chr1

32101123

-
Frame-shiftENST00000446633ENST00000373703SNRNP40chr1

31762101

-PEF1chr1

32101123

-
5CDS-5UTRENST00000446633ENST00000492061SNRNP40chr1

31762101

-PEF1chr1

32101123

-
5CDS-5UTRENST00000446633ENST00000440872SNRNP40chr1

31762101

-PEF1chr1

32101123

-

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FusionProtFeatures for SNRNP40_PEF1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SNRNP40

Q96DI7

PEF1

Q9UBV8

Component of the U5 small nuclear ribonucleoprotein(snRNP) complex. The U5 snRNP is part of the spliceosome, amultiprotein complex that catalyzes the removal of introns frompre-messenger RNAs. {ECO:0000269|PubMed:9774689}. Calcium-binding protein that acts as an adapter thatbridges unrelated proteins or stabilizes weak protein-proteincomplexes in response to calcium. Together with PDCD6, acts ascalcium-dependent adapter for the BCR(KLHL12) complex, a complexinvolved in endoplasmic reticulum (ER)-Golgi transport byregulating the size of COPII coats (PubMed:27716508). In responseto cytosolic calcium increase, the heterodimer formed with PDCD6interacts with, and bridges together the BCR(KLHL12) complex andSEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31and subsequent collagen export, which is required for neural crestspecification (PubMed:27716508). Its role in the heterodimerformed with PDCD6 is however unclear: some evidences show thatPEF1 and PDCD6 work together and promote association between PDCD6and SEC31 in presence of calcium (PubMed:27716508). Other reportsshow that PEF1 dissociates from PDCD6 in presence of calcium, andmay act as a negative regulator of PDCD6 (PubMed:11278427). Alsoacts as a negative regulator of ER-Golgi transport; possibly byinhibiting interaction between PDCD6 and SEC31 (By similarity).{ECO:0000250|UniProtKB:Q641Z8, ECO:0000269|PubMed:11278427,ECO:0000269|PubMed:27716508}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
>>>>>>>>>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-410107_146177358RepeatNote=WD 2
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-41064_103177358RepeatNote=WD 1
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05127_1388285Calcium binding1
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05194_2058285Calcium binding2
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05114_1498285DomainEF-hand 1
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05155_1838285DomainEF-hand 2
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05181_2168285DomainEF-hand 3
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05217_2538285DomainEF-hand 4
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05254_2838285DomainEF-hand 5
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0521_1098285Region9 X 9 AA approximate tandem repeat of [AP]-P-G-G-P-Y-G-G-P-P
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-05101_1098285Repeat9
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0521_298285Repeat1
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0531_398285Repeat2
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0541_498285Repeat3
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0550_588285Repeat4
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0559_678285Repeat5
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0576_848285Repeat6
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0585_928285Repeat7
TgenePEF1chr1:31762101chr1:32101123ENST00000373703-0593_1008285Repeat8

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-410149_189177358RepeatNote=WD 3
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-410191_230177358RepeatNote=WD 4
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-410233_272177358RepeatNote=WD 5
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-410283_322177358RepeatNote=WD 6
HgeneSNRNP40chr1:31762101chr1:32101123ENST00000263694-410325_357177358RepeatNote=WD 7


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FusionGeneSequence for SNRNP40_PEF1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_SNRNP40_ENST00000263694_chr1_31762101_-_PEF1_ENST00000373703_chr1_32101123_-_454aa
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIMLLSGHEGEVYCCKFHPNGSTLASAGFDRLI
LLWNVYGDCDNYATLKGHSGAVMELHYNTDGSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKGCP
GAAGQAPGAPPGSYYPGPPNSGGQYGSGLPPGGGYGGPAPGGPYGPPAGGGPYGHPNPGMFPSGTPGGPYGGAAPGGPYGQPPPSSYGAQ
QPGLYGQGGAPPNVDPEAYSWFQSVDSDHSGYISMKELKQALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQ
QYDRDRSGSISYTELQQALSQMGYNLSPQFTQLLVSRYCPRSANPAMQLDRFIQVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVTMTAS


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_SNRNP40_ENST00000263694_chr1_31762101_-_PEF1_ENST00000373703_chr1_32101123_-_1362nt
ATGATAGAACAGCAGAAGCGTAAGGGCCCAGAGTTGCCGCTGGTTCCAGTCAAGCGGCAGCGGCATGAGTTGCTGTTGGGAGCGGGGTCT
GGCCCAGGAGCCGGGCAGCAGCAGGCGACGCCGGGAGCCTTGCTGCAAGCGGGACCTCCAAGATGTTCCTCCCTTCAAGCCCCAATCATG
CTGCTCTCTGGACATGAAGGGGAAGTCTACTGCTGCAAGTTCCACCCCAACGGATCCACCTTAGCATCTGCAGGATTTGACCGACTGATA
TTACTGTGGAATGTCTATGGTGACTGTGATAACTATGCCACACTGAAGGGACACAGTGGAGCAGTGATGGAATTGCATTACAACACAGAT
GGCAGTATGCTTTTCTCAGCATCCACAGATAAAACCGTGGCTGTGTGGGATAGTGAAACAGGTGAGAGGGTTAAAAGGCTAAAGGGACAT
ACTTCCTTTGTGAATTCCTGTTATCCAGCCAGGAGAGGCCCTCAGCTTGTCTGCACTGGCAGTGACGATGGCACAGTTAAGGGCTGCCCA
GGAGCTGCAGGACAAGCACCAGGAGCCCCTCCGGGTAGCTACTACCCTGGACCCCCCAATAGTGGAGGGCAGTATGGTAGTGGGCTACCC
CCTGGTGGTGGTTATGGGGGTCCTGCCCCTGGAGGGCCTTATGGACCACCAGCTGGTGGAGGGCCCTATGGACACCCCAATCCTGGGATG
TTCCCCTCTGGAACTCCAGGAGGACCATATGGCGGTGCAGCTCCCGGGGGCCCCTATGGTCAGCCACCTCCAAGTTCCTACGGTGCCCAG
CAGCCTGGGCTTTATGGACAGGGTGGCGCCCCTCCCAATGTGGATCCTGAGGCCTACTCCTGGTTCCAGTCGGTGGACTCAGATCACAGT
GGCTATATCTCCATGAAGGAGCTAAAGCAGGCCCTGGTCAACTGCAATTGGTCTTCATTCAATGATGAGACCTGCCTCATGATGATAAAC
ATGTTTGACAAGACCAAGTCAGGCCGCATCGATGTCTACGGCTTCTCAGCCCTGTGGAAATTCATCCAGCAGTGGAAGAACCTCTTCCAG
CAGTATGACCGGGACCGCTCGGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAATGGGCTACAACCTGAGCCCCCAGTTC
ACCCAGCTTCTGGTCTCCCGCTACTGCCCACGCTCTGCCAATCCTGCCATGCAGCTTGACCGCTTCATCCAGGTGTGCACCCAGCTGCAG
GTGCTGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATTCGGCTCAGCTTCGAGGACTTCGTCACCATGACAGCTTCT


* Fusion transcript sequences (Full-length transcript).
>In-frame_SNRNP40_ENST00000263694_chr1_31762101_-_PEF1_ENST00000373703_chr1_32101123_-_2132nt
GAAGAGACCGGTTGCCGCCATGATAGAACAGCAGAAGCGTAAGGGCCCAGAGTTGCCGCTGGTTCCAGTCAAGCGGCAGCGGCATGAGTT
GCTGTTGGGAGCGGGGTCTGGCCCAGGAGCCGGGCAGCAGCAGGCGACGCCGGGAGCCTTGCTGCAAGCGGGACCTCCAAGATGTTCCTC
CCTTCAAGCCCCAATCATGCTGCTCTCTGGACATGAAGGGGAAGTCTACTGCTGCAAGTTCCACCCCAACGGATCCACCTTAGCATCTGC
AGGATTTGACCGACTGATATTACTGTGGAATGTCTATGGTGACTGTGATAACTATGCCACACTGAAGGGACACAGTGGAGCAGTGATGGA
ATTGCATTACAACACAGATGGCAGTATGCTTTTCTCAGCATCCACAGATAAAACCGTGGCTGTGTGGGATAGTGAAACAGGTGAGAGGGT
TAAAAGGCTAAAGGGACATACTTCCTTTGTGAATTCCTGTTATCCAGCCAGGAGAGGCCCTCAGCTTGTCTGCACTGGCAGTGACGATGG
CACAGTTAAGGGCTGCCCAGGAGCTGCAGGACAAGCACCAGGAGCCCCTCCGGGTAGCTACTACCCTGGACCCCCCAATAGTGGAGGGCA
GTATGGTAGTGGGCTACCCCCTGGTGGTGGTTATGGGGGTCCTGCCCCTGGAGGGCCTTATGGACCACCAGCTGGTGGAGGGCCCTATGG
ACACCCCAATCCTGGGATGTTCCCCTCTGGAACTCCAGGAGGACCATATGGCGGTGCAGCTCCCGGGGGCCCCTATGGTCAGCCACCTCC
AAGTTCCTACGGTGCCCAGCAGCCTGGGCTTTATGGACAGGGTGGCGCCCCTCCCAATGTGGATCCTGAGGCCTACTCCTGGTTCCAGTC
GGTGGACTCAGATCACAGTGGCTATATCTCCATGAAGGAGCTAAAGCAGGCCCTGGTCAACTGCAATTGGTCTTCATTCAATGATGAGAC
CTGCCTCATGATGATAAACATGTTTGACAAGACCAAGTCAGGCCGCATCGATGTCTACGGCTTCTCAGCCCTGTGGAAATTCATCCAGCA
GTGGAAGAACCTCTTCCAGCAGTATGACCGGGACCGCTCGGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAATGGGCTA
CAACCTGAGCCCCCAGTTCACCCAGCTTCTGGTCTCCCGCTACTGCCCACGCTCTGCCAATCCTGCCATGCAGCTTGACCGCTTCATCCA
GGTGTGCACCCAGCTGCAGGTGCTGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATTCGGCTCAGCTTCGAGGACTT
CGTCACCATGACAGCTTCTCGGATGCTATGACCCAACCATCTGTGGAGAGTGGAGTGCACCAGGGACCTTTCCTGGCTTCTTAGAGTGAG
AGAAGTATGTGGACATCTCTTCTTTTCCTGTCCCTCTAGAAGAACATTCTCCCTTGCTTGATGCAACACTGTTCCAAAAGAGGGTGGAGA
GTCCTGCATCATAGCCACCAAATAGTGAGGACCGGGGCTGAGGCCACACAGATAGGGGCCTGATGGAGGAGAGGATAGAAGTTGAATGTC
CTGATGGCCATGAGCAGTTGAGTGGCACAGCCTGGCACCAGGAGCAGGTCCTTGTAATGGAGTTAGTGTCCAGTCAGCTGAGCTCCACCC
TGATGCCAGTGGTGAGTGTTCATCGGCCTGTTACCGTTAGTACCTGTGTTCCCTCACCAGGCCATCCTGTCAAACGAGCCCATTTTCTCC
AAAGTGGAATCTGACCAAGCATGAGAGAGATCTGTCTATGGGACCAGTGGCTTGGATTCTGCCACACCCATAAATCCTTGTGTGTTAACT
TCTAGCTGCCTGGGGCTGGCCCTGCTCAGACAAATCTGCTCCCTGGGCATCTTTGGCCAGGCTTCTGCCCTCTGCAGCTGGGACCCCTCA
CTTGCCTGCCATGCTCTGCTCGGCTTCAGTCTCCAGGAGACAGTGGTCACCTCTCCCTGCCAATACTTTTTTTAATTTGCATTTTTTTTC


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FusionGenePPI for SNRNP40_PEF1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
SNRNP40PRPF8, SNRNP200, EFTUD2, CD2BP2, PRPF6, SNRPB2, PFDN2, MAGEA6, SF3B1, DDR1, USP39, PRPF4, CUL4A, CUL4B, WDR5, SRRM1, PML, RARA, ELAVL1, DHX16, RNU4ATAC, RNU6ATAC, APP, SNRPE, RALY, TBL1X, MDC1, EIF4A3, MAGOH, PRPF4B, RPA3, RPA2, RPA1, MOV10, NXF1, CUL7, OBSL1, SUZ12, DDX23, TSSC4, RSRC1, PRPF3, TFIP11, PAXBP1, PRPF31, SART1, ECD, SNRPD2, CCDC12, DHX38, SNRNP27, ZNHIT2, TXNL4A, AQR, SNRPD1, ISY1, RBM42, CHD3, CRNKL1, POLR3C, SREK1, XPO1, YWHAZ, USP37, SNW1, CDC5L, SNRPF, PPIE, AAR2, LMNAPEF1PDCD6, H2AFX, UBC, CUL3, LAMTOR3, PDCD6IP, DAZAP2, BAG3, NR0B2, EWSR1, HGS, CALCOCO2, TFG, CEP55, KLHL12, FOXR2, KIAA0930, HIST2H2AB, FASN, ANXA11, ENO1, ETFA, GPI, SUCLG2, CEP128, CEP164, DMRTB1, NF2


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for SNRNP40_PEF1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgenePEF1Q9UBV8DB11093Calcium CitratePeflin {ECO:0000303|PubMed:10486255}small moleculeapproved
TgenePEF1Q9UBV8DB11348Calcium PhosphatePeflin {ECO:0000303|PubMed:10486255}small moleculeapproved

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RelatedDiseases for SNRNP40_PEF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource